998-996 = 2 !!! Sorry
It is a different spec engine (storke/bore), the 998R is 999cc (and was used in the 999s when they were released - albeit a detuned one in the stock 999). The 996R had a 998cc engine - simple huh!!!
The 996R has the first of the testastretta engines and this engine was further developed for the 998R - change of stroke (shorter, means potential for higher revs). As the article says the SPS engine had been developed to the max.
In road trim there's very little difference between the 996R and 998R (although asthetically the 998R had a carbon seat unit). There's a few more BHP, but it enabled Ducati to produce a more powerful engine for racing.
My view is that the 996R is the better bike, as
1. there are fewer of them made than the 998R
2. they're the first of the testastretta engines and were handbuilt (factory were'nt set up for manufacture yet!)
3. Last and in my view most importantly - it won the WSB with Troy in 2001 - the 998R didn't.
An official release statement in 2001 - interesting about the 999R reference too!!
"At the Milan International Motorcycle Show in September 2001, Ducati pulls another ace out of its sleeve with a newly revised 998R model for the 2002 year, effectively the current 996R but with an even shorter stroke engine Testastretta motor at 104mm bore x 85.8mm stroke displacing 999cc and stock compression raised from 11.4 to 12.3:1 and rated at 139 horsepower with street tuning. The even shorter stroke engine will allow even higher RPMs and proportionally more horsepower, possibly as much as 220 hp when fully developed, and certainly more than present race tires can handle. This new short stroke Testastratta should correctly be called a 999R to differenciate it from the 998 longer stroke models, but just like the 996R, Ducati has a history of confusing us this way to tie-in the race bikes to the current streetbikes, possibly for marketing reasons. "
The 996R is a great track bike, near-linear power delivery and very stable, its better than the 996SPS for outright trackspeed (as the power is morepredictable and there's more of it). But lacks the SPS's character.
Tim